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Additional file 8. lark differential expression and GSEA analyses. Sheet1. Combined differential expression top tables for the three analyses (rnai = RNAi vs WT, uas = UAS.lark vs WT, infection = all infected vs all uninfected). Sheet2. Results of the GSEA analysis based on the logFC values of each gene and gene ontology terms acquired from go2msig.org (April 2015)

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Additional file 3. Infection-induced transcript isoform changes. Sheet1. All PSI values per transcript as calculated using MISO. RASP results for infection effect. GO results for infection effect. Differential expression results for infection effect (companion study)

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Additional file 1: Figure S1. Enteric infection leads to extensive changes in transcript isoform ratios and increased diversity. Figure S2. Example of the functional relevance of a local-sQTL. Figure S3. Post-infection transcripts tend to be longer, mainly due to the production of longer 5′ UTRs. Figure S4. Enteric infection with different pathogens leads to widespread changes in intron retention. Figure S5. Introns with increased retention have exon-like characteristics. Figure S6. Lark perturbation leads to global changes in gene expression as well as enhanced survival to infection

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Additional file 7. Intron retention results. Sheet1. Intron retention annotations and results for the DGRP lines. Sheet2. DGRP PSI table per sample. Sheet3. DGRP delta PSI table per strain. Sheet4. DGRP bayes factor table for infection effect comparisons. Sheet5. Significantly changed intron retentions in the w1118 background (Ecc15 or Pe infection). Sheet6. Intron retention events in the different lark perturbation experiments. TRUE means that the event is significantly different in the performed comparison. Sheet7. Summary of overlap with uORF by DGRP line: overlaps were calculated for all, or the significant subset of introns per DGRP strain

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Additional file 2. RNA-samples used in the study and metadata. Sheet1. DGRP RNA samples used in the study. Sheet2. w1118 RNA samples used in the study. Sheet3. lark perturbation samples used in the study

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Additional file 5. sQTL results. Sheet1. All sQTL results in both conditions (Control and Treated). Sheet2. Significant sQTL results in both conditions, along with predicted coding consequence, location within transcript, and matches to the ESE and ISE. Reference list for ESE and ISI

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Additional file 4. Shannon diversity results. Sheet1: Shannon diversity per gene per DGRP sample. Sheet2: Delta Shannon diversity (Infected – Control) per gene per DGRP line

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Additional file 6. Lengths of transcripts and effective lengths of genes. Sheet1. Lengths of transcripts and features from reference annotation. Sheet2. transcript lengths by DGRP line (taking indels into account). Sheet3. CDS lengths by DGRP line (taking indels into account). Sheet 4. 5’UTR lengths by DGRP line (taking indels into account). Sheet5. 3’UTR lengths by DGRP line (taking indels into account). Sheet6. Gene effective length by transcript (taking indels and isoform ratios into account). Sheet7. Gene effective length by 5’UTR lengths (taking indels and isoform ratios into account). Sheet8. Gene effective length by 3’UTR lengths (taking indels and isoform ratios into account)

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Additional file 9. Review history

Multiple sequence alignment of SelV and SelW.

<p>The last 9 residues of SelV exon 1 and exons 2–5 are shown aligned to complete SelW sequences. The last residue of each exon is marked in black and the Sec in red.</p